Alternatives and similar repositories for Kraken2-output-manipulation

Users that are interested in Kraken2-output-manipulation are comparing it to the libraries listed below

• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆30Updated 5 years ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆58Updated 2 months ago
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 5 years ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• allind / EukDetect
  ☆52Updated last year
• jhawkey / IS_mapper
  IS mapping software
  ☆54Updated 3 years ago
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆67Updated last month
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago
• egonozer / in_silico_pcr
  Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.
  ☆47Updated 2 months ago
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆44Updated 2 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆43Updated 2 weeks ago
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆83Updated last month
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆42Updated 7 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆41Updated 3 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆78Updated 2 weeks ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆54Updated last month
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆121Updated 3 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 9 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 10 months ago
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆59Updated 2 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆69Updated this week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• P-kai / EasyNanoMeta
  A pipeline for nanopore long-read metagenomic analysis.
  ☆38Updated last month
• EBI-Metagenomics / mettannotator
  ☆72Updated last month